Return of the Doctor's Daughter
by Skye Silverwing
Summary: The Doctor had a daughter. Her name was Jenny. Thought dead, Jenny went adventuring, and through a freak accident has found herself in Equestria. Unfortunately, her arrival triggered the greatest disaster the Ponyworld has ever seen. Rated for death.
1. Chapter 1

Return of the Doctor's Daughter

By Skye Silverwing

Chapter 1: When things get Timey-Whimey

Jenny smiled as she piloted her ship through the treacherous area of Space Known as the Dead Man's Run, where it was said that every ship to pass through mysteriously vanished.

Honestly, how could she turn down an invitation like that? If there were missing ships, then there was something making the ships disappear. And if something was making ships disappear, who better than Jenny, Daughter of the Doctor, to find out what it was and ensure that it was stopped?

It had taken her weeks to dig up the last freighter to go missing's flight plan, and a lot of flirting, sabotage, and running to get out of the Station with it. Seriously, how was she supposed to know that the alien language on the door said "Authorized personnel only, unauthorized personnel will be shot on sight."? It wasn't like she could read every language in the Universe.

Only most of them.

As she followed the course plotted through the Run, a small light began to blink on the console in front of her. Staring at the light, she tried to recall what the instruction manual had said the light meant.

She might have consulted the manual itself about the problem, but after she and it had had a disagreement about what were appropriate repairs for her to do to damaged parts of the ship, she had decided that the two of them needed to go their separate ways, and jettisoned it into the corona of a class five star.

She thought the light either meant that the sensors were picking up an unusual reading outside, or that her hot pockets were done. She could never remember which.

A quick check of her microwave telling her that there were no hot pockets for her now and therefore, the light must mean to check the sensors, so Jenny pulled down the little screen that the sensors read out on.

She cocked her head slightly. The sensors were showing a massive surge of energy heading right toward her ship. "Well, that won't do at all." She said, "Now for some running."

Turning back to the control panel in front of her, a patchwork of repairs which Jenny had done over the five years since leaving, Jenny took hold of what looked like a fishing pole attached to a lunch box (she had never bothered to actually find the right parts) she deftly piloted the ship around the energy pulse, only to find the pulse altering its course in response.

Jenny pulled down on the Soap-on-a-rope she had replaced her throttle with, increasing her speed to the fastest she could go without engaging the FTL drive. She reached her ships maximum Sub-light velocity, but the Pulse only increased in speed with her, closing at a steady rate.

Jenny grabbed the hockey stick that was embedded in the console. Piloting the ship in a series of high speed maneuvers, she lead the energy pulse on a high speed game of tag, ducking in and around groups of asteroids, through clouds of interstellar gas, and anything else that might save her from it. Unfortunately, the pulse was not slowed in the least by the obstructions, flowing around them as easily as it would through open space.

The Scanners got a reading on the pulse just before impact. It was a surge of Heuon Particles. They were being drawn to the Teleron Radiation being emitted by her FTL drive.

Jenny's mind raced with this revelation. If the Heuon Particles reacted with the Radiation in her FTL drive…

The pulse stuck the back of the ship, traveling through the multi-phasic alloy like it wasn't even there. A moment later, a warning light activated, causing Jenny to reach for the specially programmed Magic 8-ball. "What's happening?" she asked, shaking it.

A moment later, the words began to appear in its little window. "FTL drive has been activated." It said, "Warning, No course Vector set."

The FTL Drive engaged, and Jenny instantly set to several tasks. "Okay, first, scanning space to determine our course." She said, tapping commands into the console, throwing several levers and pushing a few buttons.

A warning siren sounded. A quick glance at the 8-ball told Jenny why. "Warning:" it said, "Current Trajectory analysis indicates immanent collision with class B Star."

Jenny's eyes widened slightly. "Well," she said, "That explains why starships coming through here have been disappearing. I just need to shut my FTL down before I disappear, too."

With that, she began entering the emergency shutdown codes for the FTL drive. Unfortunately the FTL was not responding, so she had only one choice. She keyed in the full shut down for the power for the entire ship. Without decelerating, the FTL dropped back into normal space hitting Space shear and shaking the ship violently, drawing showers of sparks from several of the instrument panels around her.

With the cabin having gone dark, Jenny looked out the window. It seemed that the ship had survived dropping out of FTL. Unfortunately, it was still traveling at high speed and falling directly into the star in front of it.

Jenny knew she needed to get the impulse drive back online if she wanted to avoid a fiery death, so she began the arduous process of powering the ship back up. With the star looming large in the window, and the ship traveling at just below light speed, she estimated she had only had a few minutes in which to engage the sub-light engines before there would be no avoiding the Star's Corona. This meant cutting a lot of corners in the Twenty-minute start-up procedure.

Jenny grinned. She loved cutting corners.

Without hesitating, she reactivated the power generators. They would take a minute to reach full capacity, but she could initialize other systems while it did. Inertial dampers, life support, scanners, shields, and, finally, the sub-light drive. With time ticking down, Jenny had to move quickly enough to avoid death.

As the Sub-light engines came online, she engaged them, but the scanners reported that her current Velocity was too great for the sub-light engines to stop the ship before impact. They had enough power to roll, and turn into a low orbit and slingshot her out on the other side, though.

Jenny decided that that was the best option, so she engaged the sub-light engines to execute the roll and set the shields to protect the ship from the radiation at that low an orbit. As the orbit stabilized to achieve escape velocity on the other side, Jenny began checking other systems.

A moment later, the warning light she had seen before came back on. "What now?" Jenny asked, checking her 8-ball again.

"Warning. FTL Drive activated." The ball said, "Course Vector set. Warning: Course Vector does not correspond with known dimensional vectors."

Jenny's Eyes widened. "Oh, Shi-"

The FTL engaged, and the world went white.

.o0o. .o0o. .o0o. .o0o. .o0o.

It could be said that Dr. Maretha Roan was one of the most skilled Mare Doctors in all of Equestria. She had saved dozens of lives and treated countless diseases and illnesses, making her well known in the Pony community.

What was not so well known about Maretha was that she was, in fact, a former companion of the enigmatic Stallion from another dimension; the one they called "The Doctor".

Maretha had been the one who had found him lying unconscious outside his Mysterious Box nearly ten years ago. Being a Medical Student at the time, she had attempted to administer first aide, and she had been shocked to discover that he had two hearts. It was shortly thereafter that a large number of the local mannequins came to life, and, with Maretha's assistance, the Doctor managed to stop them from hurting anypony.

After that, Maretha and the Doctor had had something of a whirlwind relationship, full of adventures as they traveled in the TARDIS, the doctor's Box, which, it had turned out, was both a starship and a time machine, and was Bigger on the inside.

They had traveled like that for a long time before Maretha realized that, though she loved him, she could not afford to spend her life with the Doctor, and she chose to leave him, and pursue her career.

The Doctor was never alone for long, however. He had four such companions since, though only the most recent, a Pegasus Pony called Derpy Hooves, had actually managed to remain with him for any decent period of time.

Maretha kept in touch, of course. They all did.

.o0o. .o0o. .o0o. .o0o. .o0o.

An insistent beeping sound drilled its way into Jenny's unconscious mind, causing her eyes to flutter open. She saw the interior of her ship, but everything that was not bolted, tied or Duct Taped down was floating. This told her that the Gravity systems had been compromised. She placed a hand on a nearby bulkhead in order to right herself, and then pushed off in order to reach the instrument panel. There was a light blinking in time with the beeping. She thought it was there to inform her that the ship was about to crash.

Sure enough, out the window was a big, shining blue, green and brown sphere. A planet obviously. It was being orbited by two moons, one of which seemed to be shining like a sun.

She had little time to ponder this impossibility of nature, though, as with each second, the planet was looming larger in the window, and it appeared that the proximity alarm was the only thing still functional.

She consulted the Magic 8-ball. "Life Support off-line, Shields off-line, graviplating off-line, Sub-light engines off-line, FTL Drive off-line." It said, "Warning: Proximity censors showing imminent impact with atmosphere of M-Class Planet. Countermeasures inoperable. Predict 90% probability of ship incineration. Abandon ship."

Jenny nodded, grabbed her pack for when she was on a planet and floated into the escape pod. She shut the door and gave one last look at the ship that had been her home for the last five years, and then she hit the button to jettison the pod, and the pod shot away.

As the ship struck the atmosphere, its hull lit up with friction and it plummeted wildly through the sky, the stresses tearing it apart.

Inside, the magic 8-ball shook violently. "Hull temperature beyond maximum limits." It said, "It has been an honor to serve you, Miss Jenny. May you find what you seek. Good-bye."

The Windows shattered and the cockpit was suddenly filled with flames for just a moment before it disintegrated entirely.

.o0o. .o0o. .o0o. .o0o. .o0o.

Twilight Sparkle, the personal student of Princess Celestia, was calmly watching the skies through her telescope. She enjoyed watching the stars as they made their nightly dance across the sky. She found it calming to study them and make notes and record their changes over time.

After her brother's wedding, she really needed calm, so she had been overjoyed the previous evening when she had noticed a new star in the night sky. She had prepared all day and had her dragon friend, Spike, gather many books and scrolls and notebooks so that she could record everything about her new star friend.

She turned her telescope to the sky, searching for the star. Her eyes widened slightly as she found it and realized that it was moving more rapidly across the sky today than it had been the previous night, a sure sign that it was far closer. As she watched, she used her magic to take notes and make observations about the object. It was moving too quickly to be a star, or a planet, for that matter, perhaps it was an asteroid?

The mysterious object in the night sky suddenly illuminated as it became engulfed in flames. Twilight smiled brightly. It had to be an asteroid, burning up in the atmosphere, and she would be watching to observe and make notes, and maybe even compare her notes with Princess Luna, who was also an avid stargazer.

She watched as a smaller object- probably a piece of the asteroid- suddenly broke off from the flaming object as it passed overhead. She had little time to note this event, however, because the main part of the object suddenly exploded in a blast the likes of which she had never seen.

Twilight looked on in horror as the enormous detonation lit up the night sky, its down blast flattening a huge portion of the Everfree Forest, and it produced a shock wave that shook Ponyville like a violent Earthquake. All over Ponyville windows shattered, trees were knocked over, and animals fled in terror.

Twilight ran from the Library as the books fell from the walls and several vases and other items fell and shattered on the floor with Spike close on her heels.

Outside, all was devastation and disarray. Several structures had collapsed, and dozens of ponies that had not been awake were now in the streets trying to figure out what had happened.

This made it that much worse when the fire started raining from the sky. Several houses, sporting thatched roofs, had ignited immediately, making taking shelter inside impossible.

Emergency Response Ponies were already fanning out through the streets, doing their best to protect the ponies in the street from the falling flames, prevent mass hysteria, dowse the fires that were starting on the buildings, and save those that were trapped.

Twilight knew that she was needed, but her eyes were drawn to the sky one last time as a streak of light shot down from the sky. It had to be the piece of the asteroid coming down. It shot over the Everfree Forest, impacting with a deep thud. Twilight made note of its direction. She would hunt it down later. She had work to do now.

.o0o. .o0o. .o0o. .o0o. .o0o.

Jenny knew she was in trouble when she saw that the ship was already deep into the atmosphere, and was burning up even as the escape pod let loose. She used the pods thrusters to attempt to put some distance between herself and the ship, but she had less than thirty seconds before the ship's antimatter reactor went up.

The resulting Explosion produced a shockwave that had knocked out the attitude controls on the pod, as well as several other systems she was sure she was going to need if she was going to land this thing safely. She was lucky that the pod still had one functioning maneuvering thruster. As the pod plummeted down onto whatever planet this was, she had the thruster fire when she could to avoid impacting anything big enough to smash the pod to pieces, and steer toward what looked like a wild area of forest. As she came in, however, the thruster finally burnt out.

Bracing herself, Jenny closed her eyes as her capsule slammed into the ground at high speed, crumpling the hull like a tin can around her and slamming Jenny hard into the bulkhead.

Jenny opened her eyes, certain that her body was broken, but she still found the strength to drag herself from the remains of the pod and make her way up the crater, stopping at a certain point and pulling herself to her knees. She looked down at her hands, confirming that they were, in fact, glowing golden as her regenerative power began to take hold. She wondered who she would become.

With that thought as the last one to enter her mind, Jenny threw her head back and screamed as the Golden light burst from her flesh, rewriting and renewing her, and collapsing the earth around the pod, burying it under the forest floor before Jenny finally collapsed in a heap.

.o0o. .o0o. .o0o. .o0o. .o0o.

The EMPs were skilled professionals, Twilight knew, but there were simply not enough of them to go around, so she hurried to the outskirts of town, where her help would be most needed, leaving Spike at the library to offer assistance to those in need and write to Celestia for aid.

Twilight reached the home of her friend Fluttershy, and gasped in shock. The big tree that grew next to the little cottage had fallen, crushing the side wall of the building.

Twilight ran over to the ruined structure. "Fluttershy!" she cried, concern filling her voice.

"Twilight!" came the response from within.

Twilight's heart leapt as she peered into the ruins, spotting her Pegasus friend stuck in the space formed by the fallen debris and her couch. "Are you alright?" she asked.

Fluttershy looked out at her, her eyes swimming with tears. "I- I'm alright…"she replied between sobs, "But- but Angel… He… He saved me."

Twilight's heart dropped into her hooves as she spotted the still form of the brave little bunny, crushed under the tree. Firming her resolve, she looked at her friend. "We can mourn him later." She said, "For now, there are ponies that need our help. I'm going to get you out of there."

Twilight flared the magic, surrounding the debris that held her friend in light, and levitated it up, freeing her.

Fluttershy, drawing strength from Twilight's resolve, pulled herself from the rubble and scuttled free of her house. The yellow pony shifted her wings slightly as Twilight checked her over. She was only sporting a few scratches and bruises, so she did a quick glance around to see how the rest of her animals were, confirming that they were mostly safe.

Fluttershy took one last look at her shattered home. "Alright, Twilight." she said, firmly for her own benefit, "Let's go save everypony."

Twilight nodded, glad that she was managing to appear so cool in this situation, in spite of being terrified. As they walked toward Sweet Apple Acres, she could not help be wonder what she would have done if she had found Fluttershy dead under that tree. Silently, she thanked Angel for his sacrifice.

The smoke that was rising in the direction of the Apple Family's farm was not a good sign, but Fluttershy suddenly gasped and ran ahead. "Rainbow Dash!" she cried.

Twilight ran after her and her heart nearly stopped when she saw the Rainbow haired Pegasus lying in the middle of the road, unmoving. A quick glance to the sky showed Twilight what had happened. The shockwave had destroyed Rainbow's cloud house completely, leaving the Pegasus in mid-air, falling through the chaotic winds that had followed.

Rainbow's left wing lay at an unnatural angle, and as Twilight approached, Fluttershy checked her for a pulse. "She's alive!" the Yellow pony announced, "But she is hurt pretty bad." She turned to the Violet unicorn. "Twilight, you go on to see if you can help Applejack at the Farm." She said, "I will take Rainbow Dash to the hospital immediately."

Twilight nodded, so proud that Fluttershy was able to function so well in this situation. With Rainbow's life on the line, she was glad her other friend was able to keep it together.

Twilight gave Fluttershy a quick farewell, and hurried on.

It took her a few minutes to round the bend and bring Sweet Apple Acres into view. It was a picture of devastation. The closest part of Ponyville to Everfree, The bulk of the Trees in the orchard had been uprooted or simply flattened. The house, the barn, and several of the outbuildings were on fire, and in the yard, Big Macintosh and Applejack tried desperately to extinguish the flames.

Seeing her approach, Applejack looked plaintively at Twilight. "Twilight!" she cried, "The house is on fire, and it's too hot to get inside! Applebloom and Granny Smith are still in there!"

Twilight nodded, her horn flaring surrounding herself and the orange earth pony in light. "This should protect us from the heat." She said, "Come on!"

Applejack nodded, and the two magic-shrouded ponies entered the inferno.

The two of them hurried up the stairs to the bedrooms. "Applebloom!" Applejack cried, "Where are you?"

A voice carried from Granny Smith's room. "Applejack!" Applebloom cried, coughing. "I'm in here! Granny Smith won't wake up! Help us!"

Applejack delivered a kick to the door, revealing the terrified filly and the utterly still form of Ponyville's oldest citizen. "Granny Smith!" Applejack cried in horror. "No…" Her voice wavered slightly, and she began to tremble, unable to contain her grief.

Twilight heard a heavy support beam in the roof groan with the loss of strength from the fire burning through it. "Applejack!" she cried, "There's no time! We have to get out! There is nothing we can do for her, but we can still get ourselves and Applebloom out. But we've got to go now!"

When Applejack failed to respond, Twilight was about to try again, but the beam over the hall outside groaned again and then broke with loud crack and collapsed, blocking the door.

Unwilling to let anyone else die here, Twilight flung magical energies around the three of them and hurled them through the nearby window, a huge blast of fire erupting behind them as they did. "NO!" Screamed Applejack, "GRANNY SMITH!"

The Orange Pony struggled against Twilight's magic, clearly intending to run back into the house in a vain attempt to save her already dead relative. Twilight bound her friend in magic, to stop her from endangering herself further. Applebloom, on the other hand, had passed out from the stress. Twilight deposited the Filly gently on the ground as Big Macintosh approached.

The Purple unicorn turned to Applejacks big brother, who seemed sullen, but resolute. "I am sorry about Granny Smith, Big Mac." She said, "But I need you to keep AJ and Applebloom out of trouble until they are not in danger anymore. Can you handle that?"

Big Macintosh simply nodded, aware that both of his sisters were going to test his resolution. "Eeyup." He said sadly.

Twilight nodded. "Good." She said, "I need to go check on the rest of the town."

With that, she took off down the road, Heading for Ponyville. She hoped against hope that her other friends were alright and that she would not have to see anyone else suffer such loss today.

.o0o. .o0o. .o0o. .o0o. .o0o.

Maretha rushed around Ponyville General Hospital as more wounded began to filter in. She and the other Doctors hurried to save those that they could. The disaster was unprecedented in Equestria's recorded history, so the Medical professionals instantly found themselves out of their depth.

Maretha winced as the sound of crying babies reached her. She turned to see a pink coated Pony with a pair of foals. Maretha instantly recognized them as Pinkie Pie and the Cake twins, Pumpkin Cake and Pound Cake.

Seeing the Doctor, Pinkie rushed over to her. "Oh, Maretha Roan!" she said, worry painting her voice, "Have you seen Mr. and Mrs. Cake? The blast knocked down Sugar Cube Corner while I was foalsitting. I haven't been able to find them yet."

Maretha gasped. "You weren't inside when it happened, were you?" she asked, attempting to ascertain if the Pink Pony was injured.

Pinkie shook her head. "My Pinkie sense warned me something bad was about to happen, so I took the foals outside." She said. "I hope Mr. and Mrs. Cake are ok. Have they been here?"

Maretha shook her head. "They have not been here, but if I see them, I will let them know you are looking for them." She said, "Why don't you take the little ones over to the Library? I hear that Cheerilee and Spike have set up a shelter there."

Suddenly, the door behind them burst open. "I need help!" The yellow coated Pegasus cried as she entered, carrying a limp blue Pegasus on her back.

Maretha gasped and hurried over, but Pinkie reached them first. "Oh, no!" the Pink Pony cried, "Fluttershy, what happened to Rainbow Dash?"

Fluttershy shivered slightly. "It looked like her cloud house was destroyed by the blast." She said. "The cloud itself was blown away."

The Implication was staggering. The city of Cloudsdale was built on similar clouds.

Maretha's eyes widened, then she took a breath and put on a professional face. "We don't have time to worry about the implications of that." She said, "Let's get Rainbow into the exam room. Once we have saved those we can reach, then we can worry about those we can't."

.o0o. .o0o. .o0o. .o0o. .o0o.

Twilight Sparkle entered the Town and was shocked to see the devastation that the explosion had wrought on the town she had come to think of as her home. She gave a long shudder when she saw the ruins of City Hall. She truly hoped that there was no one in there when it collapsed. She asked one of the EMPs where she could help, and they pointed her toward Rarity's.

When she reached the Carrousel Boutique, she stared in shock. The flimsy glass and supports structure had been flattened as well. Rarity's livelihood was destroyed, but more importantly, there were cries for help coming from within the rubble.

Twilight brought her magic to bear and began flinging beams and broken glass aside. She shifted a large chunk of rubble to the side and revealed her purple-maned unicorn friend, her usually pristine white mane stained with blood. But she was not the problem. Cradled in her hooves, lay the unmoving form of Sweetie Belle. The Filly was covered in a combination of her own and her sister's blood.

Rarity looked up at her friend plaintively. "T-Twilight…" she struggled out, "Sweetie Belle… She's–"

Twilight closed her eyes and her horn began to emit a soft light, the light enveloping Rarity's sister, and lifting her gently from the rubble. The Filly hung limply within the field of energy, not responding at all, but she was still breathing.

Twilight looked at Rarity. "She's still alive!" she told her. "Let me get you out, and then we can get the two of you to the Hospital."

Rarity shook her head. "Leave me." She said, "My… my rear legs are broken. I will only slow you down… Get Sweetie to safety."

Twilight stared at her friend in disbelief for a moment, but a cry from behind her stopped her from needing to respond.

"Oh, no, Sweetie Belle!"

Twilight turned to see a red Pegasus Filly standing not far from wear Sweetie Belle hovered, safe in the cocoon of magical light.

"Scootaloo." Twilight said, taking in the sight of the Filly and her ever-present scooter, "You should not be here. You need to get home as quick as you can. It is dangerous out here with all the debris."

The blank-flanked youth set herself defiantly. "But I want to help!" she declared, "Sweetie Belle is my friend. I can't leave her now."

Twilight was touched by the conviction in the Filly's voice. Then she had an idea. "Scootaloo, you have your Scooter." she said, "Do you think that with the wagon over there, you could get Sweetie Belle to the hospital without hurting her?"

Scootaloo's eyes widened for a moment, and then she looked at the wagon and her friend, and the look on her face became one of sure resolve. "I will do it." She said firmly. "I won't leave my friend. I will get her there safely."

With that, Scootaloo began attaching the wagon to the scooter, and Twilight turned back to the pile of rubble. "Rarity, I am going to get you out." She said firmly. "I won't leave MY friend behind anymore than Scootaloo will hers."

Rarity attempted to protest, but found herself enveloped in Twilight's magic and lifted gently from the ruins of her business. Twilight carefully placed Sweetie Belle's unconscious form on the wagon, securing her as best she could, and then nodded to Scootaloo, who began to flap her wings, creating thrust as she navigated the streets, casting an occasional worried glance back at her injured friend.

Twilight followed at a slower pace, using her magic to hold Rarity's legs still and off the ground, while steadying her and helping her follow the younger ones to the Hospital.

.o0o. .o0o. .o0o. .o0o. .o0o.

Maretha Roan was talking quietly with Pinkie Pie and Fluttershy about Rainbow Dash's condition in the Lobby of the hospital while Pound and Pumpkin slept. The Rainbow-maned Pegasus had been lucky. She had suffered a few broken bones and had some major bruising, but all evidence showed that she would be able to pull through after a little while of bed rest.

They all turned when the front door burst open and Scootaloo rode into the Lobby, being carefully mindful of a seriously injured Sweetie Belle in the wagon towed behind her scooter. "Doctor!" the young Pegasus cried, "She needs a Doctor!"

Maretha leapt to her feet and rushed to the Unicorn's side, checking Sweetie's vitals and confirming that she was badly injured. Fluttershy, following the Doctor, gasped when she saw the state of the filly, her face becoming a mask of grim resolve.

The yellow Pegasus turned to the Filly that had conveyed the wounded. "What happened?" she asked, knowing that the answer could affect how Maretha chose to treat Sweetie's injuries.

Scootaloo looked from the Pegasus to the Doctor to her friend. "She was in her sister's shop when the blast hit." She replied. "The whole place collapsed. I was looking for my friends and Twilight Sparkle had just pulled Sweetie Belle from the rubble. She suggested using my scooter to bring Sweetie here while she stayed behind to get Rarity out. They should be here soon."

Fluttershy was about to inquire into Rarity's condition when she was cut off by a groan. Sweetie Belle was coming around.

The lavender maned Unicorn shifted slightly and then opened her eyes. "Oooh…" she moaned, "What happened?"

Maretha firmly kept her from trying to sit up. "Careful, Sweetie Belle." The Pony Doctor said, "You got caught up in a disaster, and you are injured. You were lucky you survived."

Sweetie Belled shuddered slightly. "Is my sister okay?" she asked in a small voice.

Scootaloo stepped up and smiled slightly at her friend. "Twilight Sparkle is bringing her." She said, "I used my scooter to get you here faster."

Sweetie smiled at the sight of her friend, reassured, but then her eyes widened. "Scootaloo!" she cried, pausing to wince slightly as the effort aggravated her injuries, "Y-your Cutie Mark!"

The assembled ponies looked at Scootaloo, who, blushing slightly under the attention, also looked at her own flank. There, nestled in the red fur, was a clear image of Scootaloo's Scooter, with a stylized red medical cross above it.

Pinkie Pie smiled broadly. "It looks like your special talent is the transport and protection of the wounded." She said, "You are going to be a great ambulance driver, and a wonderful addition to the ranks of Ponyville's EMPs."

Scootaloo's blush was hidden by her red fur, though she was clearly uncomfortable in the spotlight. She looked at Sweetie Belle, her face suddenly becoming more firm, and addressed the concern she saw there. "I may have my Cutie Mark now, but that does not mean I am done being a Crusader." She said, "We still have to get you and Applebloom your Cutie Marks. After you get better, of course."

Sweetie Belle smiled at her friend's allaying of her unspoken fear. She was about to thank her for that when the door behind her burst open once again, revealing Twilight Sparkle and a now unconscious Rarity.

Twilight rushed the badly wounded Unicorn over to the Doctor. "Doctor Roan!" she cried, "Rarity needs your help, Right Now!"

Maretha, having ensured that none of Sweetie Belle's injuries were life-threatening, turned to look at the little one's sister.

It was immediately apparent that Rarity's injuries were far worse than those of her sister. In fact, if Maretha did not manage to perform a remarkable miracle of medical science very quickly, the bearer of the Element of Generosity would die very soon. "Nurse!" she cried, "Prep the ER! Get me every pair of hooves you can find gloved up and in there NOW!"

Twilight and the others looked on as the Nurses rushed to make the necessary preparations. "What can we do?" The Purple unicorn asked at the Doctor's retreating back.

Maretha did not pause, but gave a serious glance backward. "You can pray." She said.

.o0o. .o0o. .o0o. .o0o. .o0o.

Zecora the Zebra groaned as he dragged herself from the pile of kindling that had once been her hut. She had been lucky that her home had not been built of tougher stuff, and it had not hurt her badly when it collapsed on her. She looked at the surrounding forest, shocked to see trees that had stood for as long as she could remember felled by the same force that had devastated her hut.

She picked her way carefully through the fallen trees, trying to make her way back to civilization. Clearly the damage had spread, far and wide, so it was possible the Pony Townsfolk would need her help.

She had been going for a short time when she came upon a deep gouge in the forest floor. She was surprised to see it here, but she was more surprised to see a young, blond haired light brown-coated Filly lying at the edge of it.

Zecora approached the Filly carefully. "How odd to find a Pony child, this far out into the wild." Zecora rhymed as she checked on the Filly, "This filly girl is caked with dirt, but does not appear to be hurt."

She looked the Filly over once more and a wisp of some kind of golden mist drifted from the young one's lips, causing her to flinch back. "Inside the forest I have seen a range, but even for me this counts as strange." She said, "If something strange has laid her low, I must take her to the Ponies. They should know."

With that, the Zebra hoisted the Pony child onto her back and carried her in the direction of Ponyville.

.o0o. .o0o. .o0o. .o0o. .o0o.

The rhythmic beeping of the monitor suddenly cut off and was replaced by a steady keening. Everypony in the room reacted immediately.

"She's coding!" cried one, "Get the paddles up here!"

Another brought the Crash Cart over, charging it as she stepped forward, and announced. "CLEAR!"

All of the ponies working on the pony on the table pulled back, and the one with the defibrillator pressed the paddles to the pony's chest, sending voltage through her body with a loud thump. The ponies watched the monitor for a moment hoping it would normalize. The keening continued.

"Again!" called the surgeon.

The Defibrillator Pony stepped forward again. "CLEAR!" Again the ponies pulled back; again the paddles pressed to the dying pony's chest, again the voltage flowed through her.

They waited once more, and then one of the Doctors shook her head. "I'm calling it." She said, "She is dead."

.o0o. .o0o. .o0o. .o0o. .o0o. .o0o. .o0o. .o0o.

A.N. This has turned out far different than I envisioned it to begin with. It was not originally supposed to be a disaster fiction. Things got out of my control and now it is what it is. I tried not to have any explicitly gory scenes, though there were a fair number of deaths in this.

I want people's opinions of this one. Seriously. I am not sure how I feel about how it turned out, and if I don't get some opinions, suggestions and such, I may not continue it.


	2. Chapter 2: The Toll

Return of the Doctor's Daughter

By Skye Silverwing

Chapter 2: The Toll

Rarity gave an undignified groan as consciousness began to creep its way into the numb void of the death she had expected. Most of the last few hours, she could not recall as more than a blur, but one thing she could recall for sure was flinging herself and her magic around her sister as the roof came down, in a desperate bid to save her from crushing death, even at the cost of her own life.

Now, though, it seemed that in spite of her attempt to sacrifice it, her life was still very much in her possession. Death had no pain like this.

Forcing her eyes open, the Unicorn groaned again, but stoically refused to let the stabbing pain in her head stop her from looking around the room.

The first thing she saw was herself. Her hind legs were wrapped in heavy plaster casts and she had bandages wrapped around her body. It seemed that as badly as she had been injured, she had been treated well enough that, given time, she would recover fully.

Next her eyes turned to the bed next to hers, where she saw with no small amount of relief her sister was resting comfortably, looking considerably less injured than Rarity herself.

Rarity turned her head slightly, noticing Sweetie Belle's friend, Scootaloo, sleeping in the chair in the room. She had to admit that she was hurt to see none of her own friends showing the same level of concern over herself. She attempted to call forth her magic to bring the call button to her, but a spike of pain in her horn caused her to cry out in pain.

On the other side of the room, Scootaloo's eyes popped open. "Oh!" the filly cried, "You're awake! You had everypony worried for a while there. Oh, you shouldn't use your magic! Doctor Roan says your horn got hurt, so you should avoid using it for a few days. I'll go get Doctor Roan." She trotted quickly out of the room.

Rarity smiled a little at how grown up the Pegasus Filly was acting, but then it occurred to her that she didn't really know what was going on. Her heart sank as a thought occurred to her. What had happened to cause such a change in the young Filly?

A few moments later, Doctor Maretha Roan came in, followed by Scootaloo and a very haggard looking Twilight Sparkle.

Twilight smiled when she saw her friend's blue eyes staring back at her. "I am so glad to see you awake, Rarity." She said, "Things have been chaos since the blast."

Rarity looked at Twilight in concern. "When you say, 'blast', you mean that explosion that knocked down my home, right?" she asked, "Did it damage other parts of Ponyville as well?"

Twilight looked at her friend. "Rarity…" she said with a sigh. There was no Sugarcoating this. "That blast was probably the worst catastrophe Equestria has ever known." She used her magic to open the curtains covering the window.

Outside, the view of Ponyville was one of devastation. Many Ponies' homes lay in ruins, and there were still fires burning in the outskirts; their smoke clearly visible in the early morning Sun.

Twilight looked at her friend, stress showing clearly on her face. "The Fire Ponies are overwhelmed, the EMPs are overworked, the ERPs are being run ragged, and nopony able to help with anything has even thought about sleep in the past fourteen hours." She said. "We are working ourselves almost to death just trying to save those we can, but the death toll is terrible."

Rarity stared at her. "And you are organizing everything?" she asked, concern for her friend coloring her voice, "Surely, there is someone else… the Mayor..."

Twilight's jaw clenched slightly. "The Mayor was in City Hall." She said, looking out at the rubble where City Hall used to stand. "The ERPs managed to get her out… but… she died on the operating table last night. As of eight o'clock this morning, by order of Princess Celestia, I was made acting Mayor of Ponyville until such time as a new Mayor is chosen."

Rarity gasped. "Are…are our friends alright?" she asked.

Twilight knew who she was talking about; their friends, the other Four Bearers of the Elements of Harmony.

Twilight sighed. "It depends on what you mean by alright." She said. "Rainbow Dash is unconscious. She fell from her home when the blast struck the clouds from the sky. AJ had to be restrained and sedated. Her Granny Smith died in a fire at the farm, and she did not take it well. Fluttershy was a real trooper. Angel, her rabbit, saved her from being crushed by the tree outside her home, but died himself. She is asleep in Rainbow's hospital room. Pinkie Pie is… Well, she is Pinkie Pie, but Mr. and Mrs. Cake have not come back from their delivery to Canterlot yet, so she is taking care of the Twins."

Rarity listened with concern. "And what of aide from other parts of Equestria?" she asked.

Twilight sighed again. "Well, thanks to the quick actions of Shining Armor, Canterlot was spared damage," she said, "But their attention has to go to the hardest hit communities first."

Rarity's eyes widened. "What communities could be harder hit than Ponyville?" her eyes went back to the devastation out the window.

Twilight hung her head. "Reports are still coming in, but CloudsDale is gone." She said, drawing a gasp from the other Unicorn. "The blast wiped it from the sky. The Royal Guard are desperately searching for survivors, but they believe that we lost over ninety percent of CloudsDale's population. Hoofington is also reporting major damages, and Manehatten was hit pretty hard, too."

Rarity shook her head slightly. "That…" she said in a low, horrified voice, "That is awful. What can we do?"

Doctor Roan, who had stayed silent until now, stepped forward. "You are going to stay in bed and heal." She said simply. "The rest of us will go on tending the wounded, and then we will bury the dead. After that, we will go on. Ponies always do."

.o0o. .o0o. .o0o. .o0o. .o0o.

Zecora's mood brightened slightly when she saw that the signs of Pony civilization ahead. The Zebra had been walking all night, her progress hampered dramatically by the debris of the destruction of the forest as well as the weight of the mysterious filly she carried.

The Zebra had not really had a lot of time to ponder why the child's flesh could feel so cold, though she would have thought her dead if not for the steady rise and fall of breath in her chest.

Zecora saw the train tracks ahead and cursed the destruction for wiping out her landmarks. She must have circled north of Ponyville and was now between the Town and Canterlot. Sure enough, when she reached the clearing near the tracks, the Mountain city came into view to the North. The Pink bubble of a defensive shield clearly showed that what had happened in the forest had not been limited to it. A small concern gripped the Zebra as she turned toward Ponyville.

Hurrying along the track, Zecora made better time, quickly rounding the high bend that lead straight into Ponyville. What she saw there did not improve her concerns. It was clear that Ponyville had been hit nearly as badly as the forest, if the large piles of rubble that used to be Ponies' homes were any indication. She carried the Filly through the town, seeing that all of the Town's Emergency Workers were clearly embroiled with trying to save those that were still trapped, and determined that it would likely be best to take the child straight to the Hospital. When she reached it, she saw Twilight Sparkle talking with one of the Doctors.

Zecora approached the pair and gave an exhausted smile. "It seems good fortune that I have arrived," she rhymed, "For this filly here is yet alive."

The Doctor and Twilight both turned and rushed to see to the pair, Twilight lending support to Zecora, who was exhausted after her journey, and Maretha took the Filly from her. "Who is she?" the Doctor asked. "I have never seen her before."

Zecora gave the Mare a slight nod. "I found her on the forest floor, but of her I know nothing more." She replied, "She lives, but seems in death's own jaws. I could not even guess the cause."

Maretha looked the Filly over, shifting her body and checking her vitals. Then, a wispy golden mist began to issue from the Filly's mouth, drawing an intake of breath from the medically trained Mare in response.

Twilight gasped. "What was that?" she asked, "I have never seen anything like it."

Maretha pulled out her stethoscope and checked the pony's heart beat, then pondered for a moment. "I have." She said, "This might require a special kind of Doctor."

"What kind of Doctor?" Twilight asked.

She turned and pulled out a cellular phone, ignoring the Pony's question. "Hello, Derpy? It's Maretha Roan." She said, "Is he there?" There was a pause. "Yes, you often are when you are traveling with him." Another pause. "Well, what could possibly be that important?" her eyes widened slightly. "That many?" Another pause. "Alright, but as soon as you are done, it is important that the Doctor get here now." She then spouted off a series of numbers, checking the hospital clock as she said the last several Digits. "Let him know it has to do with him personally." Another pause. "Okay. I have to go, bye." She hung up and immediately picked up the filly and took her outside.

Twilight Sparkle started to follow her, supporting Zecora. "What was that all about?" she wanted to know, "Why did you call Derpy?"

Maretha looked at the Lavender Pony. "Twilight, you should get Zecora to the library." She said in her best "Doctor's Orders" kind of voice. "She looks like she could use the rest."

Twilight stared at her for a moment then sighed and gave a nod. "Just keep me informed, alright?" she asked, "I don't want any more trouble."

.o0o. .o0o. .o0o. .o0o. .o0o.

Inside the TARDIS (Time And Relative Dimension In Space), the Doctor chuckled as he spun a few dials threw a couple switches, and hit an apparatus that looked an awful lot like a tetherball. "So, where to now, Derpy?" he asked, a large grin on his face.

Derpy smiled broadly. The Parasprites had been a little difficult to deal with, especially when they tried to eat the TARDIS, but ultimately they had succeeded in their task of relocating the more dangerous version of them to a planet where they could no longer hurt anypony. She was about to suggest trying the Randomizer again when she remembered that Maretha Roan had called her in the middle of their adventure with some urgent matter for the Doctor.

The Derpy-eyed Pegasus Pony looked at the Doctor and smiled. "I just remembered." She said, "Maretha called. She said there was something important to do with you." She proceeded to rattle off the coordinates Maretha had given her, from memory. "She said it had to do with you personally."

The Doctor looked at Derpy and grinned. "Good old Maretha." He said happily. "Always good for an Adventure or two."

He imputed the Coordinates via a device that looked like a pinball machine, grabbed the big lever and pulled it, triggering the Vworping sound of the TARDIS's transport sequence. A moment later a deep thud told them that they had landed.

Stepping quickly to the Door, the Doctor smiled. "Come along, Derpy," he said with a flourish. "we mustn't keep dear Martha waiting."

He opened the door and stepped out into the light of day and the smile vanished from his face. Destruction and mayhem clearly were running rampant in Ponyville, and the Doctor did not like it one bit. He pulled out his Sonic Screwdriver and waved around before checking the readings. "Well, now that can't be right." He said, "This should be the second year of the Sisters, the early part of the Pony Golden Age, during the Element Protectorate. There should not be a disaster like this in this time. It makes no sense."

Spying his former companion sitting on a nearby bench with an unknown filly unconscious beside her, the Doctor hurried over. "Maretha!" He called, "What happened here?"

Maretha looked at the Doctor and shrugged. "No one knows for sure." She said, frowning. "There was a huge explosion in the sky and chaos followed. Twilight said she thought it was a meteor, and that Princess Luna is looking into it."

The Doctor checked the readings on his screwdriver once again. "It says there are Heuon Particles. Heuon particles are not supposed to exist anymore. That is just peculiar." He said, developing a massive grin. "And brilliant! Come on, Derpy, let's go investigate!"

Maretha sighed. "Doctor." She said. "As much as I know the explosion interests you, it is not the reason I called you here."

The Doctor, who had begun to wander off, turned on his heal and looked at Maretha again. "Then what is it?" he asked, clearly slightly put off by being prevented from going to investigate the strange goings on, "Come on then, don't have all day, Maretha, if you did not bring me to help with the death and destruction, why am I here?"

As if on cue, the Filly on Maretha's lap turned slightly in her sleep, expelling a small amount of golden mist.

Intrigued, the Doctor frowned and produced his stethoscope, leaning in as he listened to the blond maned brown furred filly's heartbeat. A moment later, he stepped back looking very surprised indeed. "Oh my." He said, appearing to be both excited and worried at the same time.

Maretha looked up at him. "So I'm right, then?" she asked.

The Doctor looked at the Mare and danced nervously on his toes. "Only if your hypothesis was that this filly is somehow a Time Lord." He said.

Derpy's eyes widened. "But Doctor, didn't you say that you are the last of the Time Lords?" she asked.

The Doctor pondered and danced on his toes. "Well... yes." He replied. "I… am certain all of the other Time Lords are trapped in the Time Lock, back in my home Universe, however, it stands to reason that in this Universe there could be a race of Time Ponies, which might have originated in much the same manner as the Time Lords, but differently."

The Filly began to stir, and gave a low groan. The three Ponies present turned to regard her.

Derpy smiled. "Looks like we can just ask her." She said happily.

The Doctor smiled at his assistant. "Indeed, Derpy, very astute as usual." He praised her.

The Filly groaned again and opened her eyes. Then gave a quick glance around, eyebrows rising as she realized that she was surrounded by unusual creatures. "Oh… Brilliant." She muttered.

Maretha's instincts as a doctor were first to kick in as she spoke. "How are you feeling, little one?" she asked.

The Filly's eyes widened. "Talking… Equines?" she said, "That's new."

Well there went the Doctor's theory about Time Ponies.

Derpy, of course, immediately moved to confirm. "How can talking Ponies be new?" she asked, "You are a pony the same as us, just younger."

The Filly Blinked. She held up her hoof and looked at it. "Huh." She said. "So I am. I did not know that regeneration could work like that. I was a biped before… to be fair, though, this is only the second time I needed to regenerate... I figured I would at least stay humanoid…"

Doctor Roan looked at The Doctor. The Doctor's eyes widened significantly.

Stepping closer, The Doctor looking into the Filly's eyes. "What is your name?" he asked, bringing his eyes within an inch of hers.

She looked back calmly. "I'm Jenny." She said simply.

The Doctor's eyes widened even further. "No… That is impossible." He said, "I saw you die on Messaline."

Jenny pulled back a few inches. "How could you have possibly…" she started, trailing off as she tried to figure it out.

The Medical Doctor looked carefully at The Doctor. "Who is she?" she asked.

The Doctor looked from Maretha to Derpy and back again. "She is my Daughter."

.o0o. .o0o. .o0o. .o0o. .o0o.

Rainbow Dash fluttered her eyes open, slowly stirring against the pull of several straps fastened to hold her in place. She winced as a bold of pain lanced down her wing. Slowly, she recalled waking in freefall, buffeted by winds more wild than she had ever experienced before.

She winced again when she saw the wing holding her wing in proper position for healing and bandages wrapped around her chest, but in truth she had expected far worse. Flying in those conditions would have been impossible – such forces being likely to tear a Pegasus's wings off – so she had had to close her wings and drop like a stone, flaring them only at the very last second to bleed off enough speed before she hit the ground. She had been certain of failure when her left wing had been ripped from its socket and her controlled ditch became an uncontrolled barrel roll into the ground.

Glancing around the room, she saw a sleeping Fluttershy in one of the chairs. She was glad to see her oldest friend here, but the slight look of distress on the sleeping Pony's face made her wonder if whatever had left her plunging toward her doom had caused trouble for more ponies than just her.

Glancing at her own injuries, and Fluttershy's sleeping face, she decided that the answers could wait. A little while at least.

Settling herself as comfortably as she could, given her injuries, Rainbow settled down to sleep, and wondered what other tragedies had occurred this day.

.o0o. .o0o. .o0o. .o0o. .o0o.

Twilight Sparkle studied the report that had just arrived from Canterlot. Tears welled in her eyes as she re-read the words. "Spike." She said sadly, "I need you to go get Pinkie Pie for me."

Spike nodded, and ran off. Twilight stepped to the edge of the loft and looked down at the ponies who had all at once found themselves homeless, jobless, or worse, taking refuge in her library. The numbers were staggering, and all of those who could help were doing so with everything they had to help each other.

In these bleak times, though, Twilight could not help but wonder if the strength of their friendship would be strong enough to overcome, even as the true tragedy of these events came crashing home.

It only took a few moments for Pinkie Pie to arrive. The Pink Pony carried both of the Cakes' Foals with her, their confused expressions causing Twilight to blink tears from her eyes again.

Pinkie looked at Twilight. "You needed me?" She asked.

Twilight looked out over the ponies below. "Pinkie… I…" she hesitated, "I just received word…" There was no sugar coating this. "The train Derailed on its way between Canterlot and Ponyville and went off a cliff. All those onboard were lost… Including Mr. and Mrs. Cake."

Pinkie Pie paled. "Oh, no…" she whispered, grief straining her voice. "This… This is terrible…" She scooped up the Foals and held them in a comforting hug before looking back at Twilight. "What about them?" She asked, holding up Pound and Pumpkin Cake. "Who will take care of them, feed them, bathe them, change their clothes and do all the other things their parents used to do."

Twilight looked at her friend. "Actually, after the Discord Incident, Mr. and Mrs. Cake came to me." She said. "They were concerned that if something happened to them, their Foals would not have anyone to care for them, so they asked my assistance in writing a Will. The Will names you as Pound's and Pumpkin's legal Guardian, as well as partial beneficiary of their Estate."

Pinkie Pie nuzzled the foals sadly. "I… I don't know if I can handle it…" she said, "It's such a big responsibility…"

Twilight smiled reassuringly. "Don't you worry, Pinkie Pie." She said, "I will help you all I can, and I am sure the others, and everyone else in Ponyville, will do the same. Those babies will have the whole town to care for them, not just you."

Pinkie looked reassured. "Okay…" she said softly, looking down at the Foals, "I will do my best."

Twilight smiled. "I know you will, Pinkie." She said, "Hopefully, we will be able to rebuild and move on with our lives, and give those little ones a safe home to grow up in."

.o0o. .o0o. .o0o. .o0o. .o0o.

Deep in the Everfree Forrest, the Ancient ruins of old Canterlot stood for thousands of years before Princesses Celestia had abandoned it for her new home high on the mountain. The crumbled stones, eroded by time and wind and water, as well as the life growing in the Everfree had long stood as the marker for the great power held within.

Below the surface, though, in vaults long untouched by the hand of time, and longer still passed beyond the reach of memory, a number of great cracks, deep crevasses in the stone, had appeared. From deep within, a cold green light showed, and a soft green miasma crept, rising slowly, as the air of the outside world slipped in, and deep below, something stirred.

.o0o. .o0o. .o0o. .o0o. .o0o. .o0o. .o0o.

A.N. And now the toll of the cataclysm comes to bare, and the Ponies can begin to rebuild and grieve. But of course, something Darker is on the horizon, and the Doctor and Jenny will be needed to help stop it. As always, I love constructive criticism and ideas on what should be happening. If you have a comment, I want to hear it.


End file.
